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Verbeeren J, Teixeira J, Garcia SMDA. The Muscleblind-like protein MBL-1 regulates microRNA expression in Caenorhabditis elegans through an evolutionarily conserved autoregulatory mechanism. PLoS Genet 2023; 19:e1011109. [PMID: 38134228 PMCID: PMC10773944 DOI: 10.1371/journal.pgen.1011109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 01/08/2024] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
The Muscleblind-like (MBNL) family is a highly conserved set of RNA-binding proteins (RBPs) that regulate RNA metabolism during the differentiation of various animal tissues. Functional insufficiency of MBNL affects muscle and central nervous system development, and contributes to the myotonic dystrophies (DM), a set of incurable multisystemic disorders. Studies on the regulation of MBNL genes are essential to provide insight into the gene regulatory networks controlled by MBNL proteins and to understand how dysregulation within these networks causes disease. In this study, we demonstrate the evolutionary conservation of an autoregulatory mechanism that governs the function of MBNL proteins by generating two distinct protein isoform types through alternative splicing. Our aim was to further our understanding of the regulatory principles that underlie this conserved feedback loop in a whole-organismal context, and to address the biological significance of the respective isoforms. Using an alternative splicing reporter, our studies show that, during development of the Caenorhabditis elegans central nervous system, the orthologous mbl-1 gene shifts production from long protein isoforms that localize to the nucleus to short isoforms that also localize to the cytoplasm. Using isoform-specific CRISPR/Cas9-generated strains, we showed that expression of short MBL-1 protein isoforms is required for healthy neuromuscular function and neurodevelopment, while expression of long MBL-1 protein isoforms is dispensable, emphasizing a key role for cytoplasmic functionalities of the MBL-1 protein. Furthermore, RNA-seq and lifespan analyses indicated that short MBL-1 isoforms are crucial regulators of miRNA expression and, in consequence, required for normal lifespan. In conclusion, this study provides support for the disruption of cytoplasmic RNA metabolism as a contributor in myotonic dystrophy and paves the way for further exploration of miRNA regulation through MBNL proteins during development and in disease models.
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Affiliation(s)
- Jens Verbeeren
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Joana Teixeira
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
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Matilainen O, Ribeiro ARS, Verbeeren J, Cetinbas M, Sood H, Sadreyev RI, Garcia SMDA. Loss of muscleblind splicing factor shortens Caenorhabditis elegans lifespan by reducing the activity of p38 MAPK/PMK-1 and transcription factors ATF-7 and Nrf/SKN-1. Genetics 2021; 219:6325509. [PMID: 34849877 PMCID: PMC8633093 DOI: 10.1093/genetics/iyab114] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/03/2021] [Indexed: 12/13/2022] Open
Abstract
Muscleblind-like splicing regulators (MBNLs) are RNA-binding factors that have an important role in developmental processes. Dysfunction of these factors is a key contributor of different neuromuscular degenerative disorders, including Myotonic Dystrophy type 1 (DM1). Since DM1 is a multisystemic disease characterized by symptoms resembling accelerated aging, we asked which cellular processes do MBNLs regulate that make them necessary for normal lifespan. By utilizing the model organism Caenorhabditis elegans, we found that loss of MBL-1 (the sole ortholog of mammalian MBNLs), which is known to be required for normal lifespan, shortens lifespan by decreasing the activity of p38 MAPK/PMK-1 as well as the function of transcription factors ATF-7 and SKN-1. Furthermore, we show that mitochondrial stress caused by the knockdown of mitochondrial electron transport chain components promotes the longevity of mbl-1 mutants in a partially PMK-1-dependent manner. Together, the data establish a mechanism of how DM1-associated loss of muscleblind affects lifespan. Furthermore, this study suggests that mitochondrial stress could alleviate symptoms caused by the dysfunction of muscleblind splicing factor, creating a potential approach to investigate for therapy.
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Affiliation(s)
- Olli Matilainen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00790, Finland
| | - Ana R S Ribeiro
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00790, Finland
| | - Jens Verbeeren
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00790, Finland
| | - Murat Cetinbas
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Heini Sood
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00790, Finland
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Susana M D A Garcia
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00790, Finland
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Nikonova E, Kao SY, Ravichandran K, Wittner A, Spletter ML. Conserved functions of RNA-binding proteins in muscle. Int J Biochem Cell Biol 2019; 110:29-49. [PMID: 30818081 DOI: 10.1016/j.biocel.2019.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 02/21/2019] [Accepted: 02/23/2019] [Indexed: 12/13/2022]
Abstract
Animals require different types of muscle for survival, for example for circulation, motility, reproduction and digestion. Much emphasis in the muscle field has been placed on understanding how transcriptional regulation generates diverse types of muscle during development. Recent work indicates that alternative splicing and RNA regulation are as critical to muscle development, and altered function of RNA-binding proteins causes muscle disease. Although hundreds of genes predicted to bind RNA are expressed in muscles, many fewer have been functionally characterized. We present a cross-species view summarizing what is known about RNA-binding protein function in muscle, from worms and flies to zebrafish, mice and humans. In particular, we focus on alternative splicing regulated by the CELF, MBNL and RBFOX families of proteins. We discuss the systemic nature of diseases associated with loss of RNA-binding proteins in muscle, focusing on mis-regulation of CELF and MBNL in myotonic dystrophy. These examples illustrate the conservation of RNA-binding protein function and the marked utility of genetic model systems in understanding mechanisms of RNA regulation.
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Affiliation(s)
- Elena Nikonova
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Shao-Yen Kao
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Keshika Ravichandran
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Anja Wittner
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Maria L Spletter
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany; Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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Antonacci S, Forand D, Wolf M, Tyus C, Barney J, Kellogg L, Simon MA, Kerr G, Wells KL, Younes S, Mortimer NT, Olesnicky EC, Killian DJ. Conserved RNA-binding proteins required for dendrite morphogenesis in Caenorhabditis elegans sensory neurons. G3 (BETHESDA, MD.) 2015; 5:639-53. [PMID: 25673135 PMCID: PMC4390579 DOI: 10.1534/g3.115.017327] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/09/2015] [Indexed: 01/22/2023]
Abstract
The regulation of dendritic branching is critical for sensory reception, cell-cell communication within the nervous system, learning, memory, and behavior. Defects in dendrite morphology are associated with several neurologic disorders; thus, an understanding of the molecular mechanisms that govern dendrite morphogenesis is important. Recent investigations of dendrite morphogenesis have highlighted the importance of gene regulation at the posttranscriptional level. Because RNA-binding proteins mediate many posttranscriptional mechanisms, we decided to investigate the extent to which conserved RNA-binding proteins contribute to dendrite morphogenesis across phyla. Here we identify a core set of RNA-binding proteins that are important for dendrite morphogenesis in the PVD multidendritic sensory neuron in Caenorhabditis elegans. Homologs of each of these genes were previously identified as important in the Drosophila melanogaster dendritic arborization sensory neurons. Our results suggest that RNA processing, mRNA localization, mRNA stability, and translational control are all important mechanisms that contribute to dendrite morphogenesis, and we present a conserved set of RNA-binding proteins that regulate these processes in diverse animal species. Furthermore, homologs of these genes are expressed in the human brain, suggesting that these RNA-binding proteins are candidate regulators of dendrite development in humans.
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Affiliation(s)
- Simona Antonacci
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Daniel Forand
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado 80918
| | - Margaret Wolf
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Courtney Tyus
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Julia Barney
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Leah Kellogg
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Margo A Simon
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Genevieve Kerr
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Kristen L Wells
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Serena Younes
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado 80918
| | - Nathan T Mortimer
- Department of Biological Sciences, University of Denver, Denver, Colorado 80208
| | - Eugenia C Olesnicky
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado 80918
| | - Darrell J Killian
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
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Garcia-Alcover I, López Castel A, Perez-Alonso M, Artero R. In vivo strategies for drug discovery in myotonic dystrophy disorders. DRUG DISCOVERY TODAY. TECHNOLOGIES 2013; 10:e97-102. [PMID: 24050236 DOI: 10.1016/j.ddtec.2012.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Myotonic dystrophy (DM) is a complex neuromuscular genetic disease for which there is currently no valid therapy. The recent development of non-mammal animal models opened up the possibility of performing drug discovery in vivo, using as screening readout phenotypes with underlying molecular parallels to the disease. In this review we discuss the state of the art technologies already used in large scale drug screening and provide guidance for further development of novel technologies.
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Chen PH, Hsiao KM, Chou CC. Molecular characterization of toxicity mechanism of single-walled carbon nanotubes. Biomaterials 2013; 34:5661-9. [PMID: 23623425 DOI: 10.1016/j.biomaterials.2013.03.093] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 03/29/2013] [Indexed: 11/30/2022]
Abstract
Carbon nanotubes (CNTs) are one of widely used nanomaterials in industry and biomedicine. The potential impact of single-walled carbon nanotubes (SWCNTs) was evaluated using Caenorhabditis elegans (C. elegans) as a toxicological animal model. SWCNTs are extremely hydrophobic to form large agglomerates in aqueous solutions. Highly soluble amide-modified SWCNTs (a-SWCNTs) were therefore used in the present study so that the exact impact of SWCNTs could be studied. No significant toxicity was observed in C. elegans due to the amide modification. a-SWCNTs were efficiently taken up by worms and caused acute toxicity, including retarded growth, shortened lifespan and defective embryogenesis. The resulting toxicity was reversible since C. elegans could recover from a-SWCNT-induced toxicity once the exposure terminates. Chronic exposure to low doses of a-SWCNTs during all development stages could also cause a toxic accumulation in C. elegans. Genome-wide gene expression analysis was performed to investigate the toxic molecular mechanisms. Functional genomic analysis and molecular biology validation suggest that defective endocytosis, the decreased activity of the citrate cycle and the reduced nuclear translocation of DAF-16 transcription factor play key roles in inducing the observed a-SWCNT toxicity in worms. The present study presents an integrated approach to evaluating the toxicity of nanomaterials at the organism and molecular level for human and environmental health and demonstrates that traditional toxicological endpoints associated with functional genomic analysis can provide global and thorough insight into toxicity.
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Affiliation(s)
- Po-Hsuan Chen
- Department of Life Science and Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi 62102, Taiwan.
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Llamusi B, Bargiela A, Fernandez-Costa JM, Garcia-Lopez A, Klima R, Feiguin F, Artero R. Muscleblind, BSF and TBPH are mislocalized in the muscle sarcomere of a Drosophila myotonic dystrophy model. Dis Model Mech 2012; 6:184-96. [PMID: 23118342 PMCID: PMC3529350 DOI: 10.1242/dmm.009563] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a genetic disease caused by the pathological expansion of a CTG trinucleotide repeat in the 3′ UTR of the DMPK gene. In the DMPK transcripts, the CUG expansions sequester RNA-binding proteins into nuclear foci, including transcription factors and alternative splicing regulators such as MBNL1. MBNL1 sequestration has been associated with key features of DM1. However, the basis behind a number of molecular and histological alterations in DM1 remain unclear. To help identify new pathogenic components of the disease, we carried out a genetic screen using a Drosophila model of DM1 that expresses 480 interrupted CTG repeats, i(CTG)480, and a collection of 1215 transgenic RNA interference (RNAi) fly lines. Of the 34 modifiers identified, two RNA-binding proteins, TBPH (homolog of human TAR DNA-binding protein 43 or TDP-43) and BSF (Bicoid stability factor; homolog of human LRPPRC), were of particular interest. These factors modified i(CTG)480 phenotypes in the fly eye and wing, and TBPH silencing also suppressed CTG-induced defects in the flight muscles. In Drosophila flight muscle, TBPH, BSF and the fly ortholog of MBNL1, Muscleblind (Mbl), were detected in sarcomeric bands. Expression of i(CTG)480 resulted in changes in the sarcomeric patterns of these proteins, which could be restored by coexpression with human MBNL1. Epistasis studies showed that Mbl silencing was sufficient to induce a subcellular redistribution of TBPH and BSF proteins in the muscle, which mimicked the effect of i(CTG)480 expression. These results provide the first description of TBPH and BSF as targets of Mbl-mediated CTG toxicity, and they suggest an important role of these proteins in DM1 muscle pathology.
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Affiliation(s)
- Beatriz Llamusi
- Translational Genomics Group, Department of Genetics, University of Valencia, Doctor Moliner 50, 46100 Burjasot, Valencia, Spain
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Spilker KA, Wang GJ, Tugizova MS, Shen K. Caenorhabditis elegans Muscleblind homolog mbl-1 functions in neurons to regulate synapse formation. Neural Dev 2012; 7:7. [PMID: 22314215 PMCID: PMC3353867 DOI: 10.1186/1749-8104-7-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 02/07/2012] [Indexed: 01/08/2023] Open
Abstract
Background The sequestration of Muscleblind splicing regulators results in myotonic dystrophy. Previous work on Muscleblind has largely focused on its roles in muscle development and maintenance due to the skeletal and cardiac muscle degeneration phenotype observed in individuals with the disorder. However, a number of reported nervous system defects suggest that Muscleblind proteins function in other tissues as well. Results We have identified a mutation in the Caenorhabditis elegans homolog of Muscleblind, mbl-1, that is required for proper formation of neuromuscular junction (NMJ) synapses. mbl-1 mutants exhibit selective loss of the most distal NMJ synapses in a C. elegans motorneuron, DA9, visualized using the vesicle-associated protein RAB-3, as well as the active zone proteins SYD-2/liprin-α and UNC-10/Rim. The proximal NMJs appear to have normal pre- and postsynaptic specializations. Surprisingly, expressing a mbl-1 transgene in the presynaptic neuron is sufficient to rescue the synaptic defect, while muscle expression has no effect. Consistent with this result, mbl-1 is also expressed in neurons. Conclusions Based on these results, we conclude that in addition to its functions in muscle, the Muscleblind splice regulators also function in neurons to regulate synapse formation.
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Affiliation(s)
- Kerri A Spilker
- Department of Biology, Howard Hughes Medical Institute, Stanford University, 385 Serra Mall, Stanford, California 94305, USA
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Fernandez-Costa JM, Llamusi MB, Garcia-Lopez A, Artero R. Alternative splicing regulation by Muscleblind proteins: from development to disease. Biol Rev Camb Philos Soc 2011; 86:947-58. [PMID: 21489124 DOI: 10.1111/j.1469-185x.2011.00180.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Regulated use of exons in pre-mRNAs, a process known as alternative splicing, strongly contributes to proteome diversity. Alternative splicing is finely regulated by factors that bind specific sequences within the precursor mRNAs. Members of the Muscleblind (Mbl) family of splicing factors control critical exon use changes during the development of specific tissues, particularly heart and skeletal muscle. Muscleblind homologs are only found in metazoans from Nematoda to mammals. Splicing targets and recognition mechanisms are also conserved through evolution. In this recognition, Muscleblind CCCH-type zinc finger domains bind to intronic motifs in pre-mRNA targets in which the protein can either activate or repress splicing of nearby exons, depending on the localization of the binding motifs relative to the regulated alternative exon. In humans, the Muscleblind-like 1 (MBNL1) proteins play a critical role in hereditary diseases caused by microsatellite expansions, particularly myotonic dystrophy type 1 (DM1), in which depletion of MBNL1 activity through sequestration explains most misregulated alternative splicing events, at least in murine models. Because of the involvement of these proteins in human diseases, further understanding of the molecular mechanisms by which MBNL1 regulates splicing will help design therapies to revert pathological splicing alterations. Here we summarize the most relevant findings on this family of proteins in recent years, focusing on recently described functional motifs, transcriptional regulation of Muscleblind, regulatory activity on splicing, and involvement in human diseases.
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Wang LC, Chen KY, Pan H, Wu CC, Chen PH, Liao YT, Li C, Huang ML, Hsiao KM. Muscleblind participates in RNA toxicity of expanded CAG and CUG repeats in Caenorhabditis elegans. Cell Mol Life Sci 2011; 68:1255-67. [PMID: 20848157 PMCID: PMC11114631 DOI: 10.1007/s00018-010-0522-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 08/06/2010] [Accepted: 08/30/2010] [Indexed: 01/22/2023]
Abstract
We have utilized Caenorhabditis elegans as a model to investigate the toxicity and underlying mechanism of untranslated CAG repeats in comparison to CUG repeats. Our results indicate that CAG repeats can be toxic at the RNA level in a length-dependent manner, similar to that of CUG repeats. Both CAG and CUG repeats of toxic length form nuclear foci and co-localize with C. elegans muscleblind (CeMBL), implying that CeMBL may play a role in repeat RNA toxicity. Consistently, the phenotypes of worms expressing toxic CAG and CUG repeats, including shortened life span and reduced motility rate, were partially reversed by CeMbl over-expression. These results provide the first experimental evidence to show that the RNA toxicity induced by expanded CAG and CUG repeats can be mediated, at least in part, through the functional alteration of muscleblind in worms.
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Affiliation(s)
- Li-Chun Wang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, 402 Taiwan
| | - Kuan-Yu Chen
- Institute of Biotechnology, National Cheng Kung University, Tainan, 701 Taiwan
| | - Huichin Pan
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, 402 Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, 402 Taiwan
| | - Chia-Chieh Wu
- Institute of Molecular Biology, National Chung Cheng University, Chia-Yi, 621 Taiwan
| | - Po-Hsuan Chen
- Institute of Molecular Biology, National Chung Cheng University, Chia-Yi, 621 Taiwan
| | - Yuan-Ting Liao
- Institute of Molecular Biology, National Chung Cheng University, Chia-Yi, 621 Taiwan
| | - Chin Li
- Institute of Molecular Biology, National Chung Cheng University, Chia-Yi, 621 Taiwan
- Department of Life Science, National Chung Cheng University, 168, University Road, Min-Hsiung, Chia-Yi, 62102 Taiwan, ROC
| | - Min-Lang Huang
- Institute of Molecular Biology, National Chung Cheng University, Chia-Yi, 621 Taiwan
- Department of Life Science, National Chung Cheng University, 168, University Road, Min-Hsiung, Chia-Yi, 62102 Taiwan, ROC
| | - Kuang-Ming Hsiao
- Institute of Molecular Biology, National Chung Cheng University, Chia-Yi, 621 Taiwan
- Department of Life Science, National Chung Cheng University, 168, University Road, Min-Hsiung, Chia-Yi, 62102 Taiwan, ROC
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Sasagawa N, Ohno E, Kino Y, Watanabe Y, Ishiura S. Identification ofCaenorhabditis elegansK02H8.1 (CeMBL), a functional ortholog of mammalian MBNL proteins. J Neurosci Res 2009; 87:1090-7. [DOI: 10.1002/jnr.21942] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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